Fig. 5

The number of genes recovered by SLAM-seq correlates with read depth. Lineplot comparing the number of genes recovered post-filtering and initial read depth. SLAM-seq data was derived from strain RDY73 treated with 4-thiouracil (4tU) for 4 min. T > C read counts were normalized using size factors calculated on total read counts from exogenous whole cell spike-in. Genes were filtered as described in Materials and Procedure (relaxed filtering; dark blue line) or on the requirement that genes have ≥ one T > C read count across all samples (n = 6) (strict filtering; light blue line). Genes classified as dubious open reading frames (ORFs) or pseudogenes were removed in both filtering procedures. To adjust initial read depth, reads were randomly subsampled prior to SLAM-DUNK processing (see Materials and Procedure)